Transcriptomics provides valuable data for functional annotations of genes, the discovery of biomarkers, and quantitative assessment of responses to challenges. Meta-analysis of Nofima’s Atlantic salmon microarray database was performed for the selection of genes that have shown strong and reproducible expression changes. Using data from 127 experiments including 6440 microarrays, four transcription modules (TM) were identified with a total of 902 annotated genes: 161 virus responsive genes – VRG (activated with five viruses and poly I:C), genes that responded to three pathogenic bacteria (523 up and 33 down-regulated genes), inflammation not caused by infections – wounds, melanized foci in skeletal muscle and exposure to PAMP (180 up and 72 down-regulated genes), and stress by exercise, crowding and cortisol implants (33 genes). To assist the selection of gene markers, genes in each TM were ranked according to the scale of expression changes. In terms of functional annotations, association with diseases and stress was unknown or not reflected in public databases for a large part of genes, including several genes with the highest ranks. A set of multifunctional genes was discovered. Cholesterol 25-hydroxylase was present in all TM and 22 genes, including most differentially expressed matrix metalloproteinases 9 and 13 were assigned to three TMs. The meta-analysis has improved understanding of the defense strategies in Atlantic salmon. VRG have demonstrated equal or similar responses to RNA (SAV, IPNV, PRV, and ISAV), and DNA (gill pox) viruses, injection of bacterial DNA (plasmid) and exposure of cells to PAMP (CpG and gardiquimod) and relatively low sensitivity to inflammation and bacteria. Genes of the highest rank show preferential expression in erythrocytes. This group includes multigene families (gig and several trim families) and many paralogs. Of pathogen recognition receptors, only RNA helicases have shown strong expression changes. Most VRG (82%) are effectors with a preponderance of ubiquitin-related genes, GTPases, and genes of nucleotide metabolism. Many VRG have unknown roles. The identification of TMs makes possible quantification of responses and assessment of their interactions. Based on this, we are able to separate pathogen-specific responses from general inflammation and stress.

转录组学为基因的功能注释、生物标志物的发现和对挑战的反应的定量评估提供了有价值的数据。对 Nofima 的大西洋鲑鱼微阵列数据库进行了荟萃分析，以选择表现出强烈和可重复表达变化的基因。使用来自包括 6440 个微阵列在内的 127 个实验的数据，确定了四个转录模块 (TM)，总共有 902 个注释基因：161 个病毒响应基因——VRG（用五种病毒和 poly I:C 激活），对三种病原菌有反应的基因（523 个上调基因和 33 个下调基因）、非感染引起的炎症——伤口、骨骼肌中的黑色素灶和暴露于 PAMP（180 个上调基因和 72 个下调基因），以及运动、拥挤和皮质醇植入引起的压力（33基因）。为了帮助选择基因标记，每个 TM 中的基因根据表达变化的规模进行排序。在功能注释方面，大部分基因与疾病和压力的关联未知或未反映在公共数据库中，其中包括几个排名最高的基因。发现了一组多功能基因。胆固醇 25-羟化酶存在于所有 TM 和 22 个基因中，包括大多数差异表达的基质金属蛋白酶 9 和 13 被分配到三个 TM。元分析提高了对大西洋鲑鱼防御策略的理解。VRG 对 RNA（SAV、IPNV、PRV 和 ISAV）和 DNA（鳃痘）病毒表现出相同或相似的反应，注射细菌 DNA（质粒）和细胞暴露于 PAMP（CpG 和 gardiquimod）以及对炎症和细菌的敏感性相对较低。最高等级的基因在红细胞中优先表达。该组包括多基因家族（gig 和几个修剪家族）和许多旁系同源物。在病原体识别受体中，只有 RNA 解旋酶表现出强烈的表达变化。大多数 VRG (82%) 是泛素相关基因、GTP 酶和核苷酸代谢基因占优势的效应物。许多 VRG 都有未知的角色。TM 的识别使得响应的量化和它们的相互作用的评估成为可能。基于此，我们能够将病原体特异性反应与一般炎症和压力分开。该组包括多基因家族（gig 和几个修剪家族）和许多旁系同源物。在病原体识别受体中，只有 RNA 解旋酶表现出强烈的表达变化。大多数 VRG (82%) 是泛素相关基因、GTP 酶和核苷酸代谢基因占优势的效应物。许多 VRG 都有未知的角色。TM 的识别使得响应的量化和它们的相互作用的评估成为可能。基于此，我们能够将病原体特异性反应与一般炎症和压力分开。该组包括多基因家族（gig 和几个修剪家族）和许多旁系同源物。在病原体识别受体中，只有 RNA 解旋酶表现出强烈的表达变化。大多数 VRG (82%) 是泛素相关基因、GTP 酶和核苷酸代谢基因占优势的效应物。许多 VRG 都有未知的角色。TM 的识别使得响应的量化和它们的相互作用的评估成为可能。基于此，我们能够将病原体特异性反应与一般炎症和压力分开。许多 VRG 都有未知的角色。TM 的识别使得响应的量化和它们的相互作用的评估成为可能。基于此，我们能够将病原体特异性反应与一般炎症和压力分开。许多 VRG 都有未知的角色。TM 的识别使得响应的量化和它们的相互作用的评估成为可能。基于此，我们能够将病原体特异性反应与一般炎症和压力分开。